Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-03-24T17:28:05ZEcoinformatics Redmine
Redmine Kepler - Bug #3183 (New): Return/Enter does not select default button in dialog boxeshttps://projects.ecoinformatics.org/ecoinfo/issues/31832008-03-24T17:28:05ZSean Riddleswriddle@gmail.com
<p>Pressing Return/Enter does not select the default button (usually 'Commit') of dialogs. This should be the case according to the Apple human interface guidelines.</p> Kepler - Bug #3106 (New): Out of memory while opening all demos, is -Xss5m or SVG the problem?https://projects.ecoinformatics.org/ecoinfo/issues/31062008-01-29T04:54:18ZChristopher Brookscxh@eecs.berkeley.edu
<p>I'm marking this as having a target milestone of 1.0.0rc1 because<br />I suspect we should remove -Xss5m from build.xml because it means<br />we cannot open up very many models. Once that is addressed, the<br />milestone should be changed to something later.</p>
<p>Under Windows XP with Java 1.5.0_11, Kepler runs out of memory when opening all the demos whereas Ptolemy does not.</p>
<p>It could be that SVG is the issue, or it could be because Kepler<br />does not do lazy evaluation and thus loads in everything.</p>
<p>To replicate<br />1) Start Kepler with "ant run-dev", which uses -Xmx512m<br />2) Help -> Documentation -> Ptolemy Documentation -> Acknowledgements<br />3) Click on the copyright link at the bottom<br />4) Click on copyrights in<br />"Other copyrights about this configuration (may take a moment to run)." <br />5) Click on about in<br />"Other information about this configuration." <br />6) In the "ptolemy/configs/doc/completeDemosPtinyKepler.htm" line, click on<br /> "Open the .htm, .html, .xml and .pdf "</p>
<p>Roughly 25 windows will open and eventually, we get:</p>
<p>Caused by: java.lang.OutOfMemoryError: unable to create new native thread<br /> at java.lang.Thread.start0(Native Method)</p>
<p>Under Windows, the task manager says we are using 330Mb of memory,</p>
<p>Editing the run-dev entry in build.xml and removing:<br /><jvmarg value="-Xss5m"/><br />means we get to 580Mb in the task manager and then Kepler hangs with the<br />CPU Usage at 99%</p>
<p>java -X says that -Xss<br />-Xss<size> set java thread stack size</p>
<p>Perhaps -Xss should be removed from build.xml?</p>
<p>If I increase the Xmx from 512 to 1024, then the show all demos works,<br />At the end the amount of memory reported by the Task Manager is <br />258Mb, with a max of 608Mb<br />Running the last demo (sr/demo/TrafficLight/TrafficLight.xml) shows<br />this memory usage under Kepler:<br /> [java] 14471 ms. Memory: 968096K Free: 211261K (22%)</p>
<p>In contrast, doing the same thing with Ptolemy (no SVG), the task<br />manager reports 142Mb with a max of 142Mb. Running the same demo<br />reports:<br />6780 ms. Memory: 117172K Free: 24710K (21%)</p> Kepler - Bug #2452 (New): consider providing management console for workflow engineerhttps://projects.ecoinformatics.org/ecoinfo/issues/24522006-06-02T19:25:56ZLaura Downeyldowney@lternet.edu
<p>Consider providing a management console for the workflow engineer – for feedback and status during running of a workflow, possibly even understanding how the process was distributed across nodes, this feature could also include a parts list of every component in a workflow, might even have a “dry-run†button that would allow people to prep the workflow for running, also consider adding provenance data or access to provenance data from the management console.</p> Kepler - Bug #2414 (New): Opening a preexisting model should open in a blank viewerhttps://projects.ecoinformatics.org/ecoinfo/issues/24142006-04-13T21:42:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>In "add welcome screen for release 1.0" at<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343</a></p>
<p>Matthew wrote:</p>
<blockquote>
<p>Now this has been added, here is a very common use case, which seems incorrect<br />(reported by Kevin):</p>
<p>1) User starts kepler - gets blank graph frame, with new welcome screen in front</p>
<p>2) User dismisses welcome screen, and is left with blank graph frame</p>
<p>3) User then does "File->Open" and opens an existing workflow</p>
<p>4) The workflow then opens in a <strong>new</strong> graph frame, leaving the original, empty <br />graph frame on the screen.</p>
<p>Proposed resolution:</p>
<p>BEST: at startup, if user does the above, then the workflow gets opened in the<br /><strong>existing</strong> blank graph frame. Subsequently-opened workflows open up in <strong>new</strong><br />graph frames, as before</p>
</blockquote>
<blockquote>
<p>INTERIM: if we don't have time to implement the above for this release, then<br />check to see if we are in the above use-case, and if so, close the blank graph<br />frame after the first workflow has been opened</p>
<p>Any other thoughts/comments/ideas?</p>
</blockquote>
<p>I wrote:</p>
<blockquote>
<p>Probably File Open should be smart enough to realize that the current window<br />is mostly blank and a candidate for replacement. I'm not sure if<br />this will be very easy. For example, when one does File -> Save As, and<br />uses a new name, a new window appears. We need to handle "Unnamed" models<br />specially. I can take a look at this at some point, but probably not before<br />early March.</p>
</blockquote>
<p>I won't have time before Kepler 1.0, so I'm opening this as a separate <br />enhancement. This new bug has to do with the blank or Unnamed models,<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2343</a><br />has to do with the welcome window.</p> Kepler - Bug #2410 (New): need feature in UI for users to assign icon to an actorhttps://projects.ecoinformatics.org/ecoinfo/issues/24102006-04-11T20:21:14ZLaura Downeyldowney@lternet.edu
<p>If a user creates an R actor, there is currently no method for them to assign an icon to the R actor from the user interface. They currently get the default "R" icon but the plan is to offer a family of R actors where another more functional icon can be chosen to represent exactly what the R expression is doing for that particular R actor.</p>
<p>This is requested for after 1.0 release.</p> Kepler - Bug #2397 (New): TOOLTIPS: dual screen setup - tooltip sometimes shown on wrong screenhttps://projects.ecoinformatics.org/ecoinfo/issues/23972006-04-05T21:20:22ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Moved to its own bug from Bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: tool tip problems (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1844">#1844</a> -</p>
<p>Reported by Laura Downey <<a class="email" href="mailto:ldowney@lternet.edu">ldowney@lternet.edu</a>>:<br />------------------------------------------------<br />In operating on a dual screen PC sometimes the tool tip displays on the opposite screen from which the mouse cursor is located (and hovering over an object).</p>
<p>[MB's note: I think this is probably a JVM bug. Anyone have any additional info, or specific test cases?]</p> Kepler - Bug #2393 (New): Need ability to disable 'add port' to actors where not supportedhttps://projects.ecoinformatics.org/ecoinfo/issues/23932006-04-03T21:52:01ZDan Higginshiggins@nceas.ucsb.edu
<p>Currently one can 'add a port' to any actor even when that actor is not designed to look for new ports. This has confused some new users. It would be useful if there was a way to disable the add port button for individual actors (or enable it for only certain actors!)</p> Kepler - Bug #2362 (In Progress): DataSourceIcon: use new SVG Icons dynamically, instead of drawi...https://projects.ecoinformatics.org/ecoinfo/issues/23622006-02-21T00:55:39ZMatthew Brookebrooke@nceas.ucsb.edu
<p>org.ecoinformatics.seek.datasource.DataSourceIcon (used by the EML200DataSource<br />actor, among others) draws its own icon dynamically - changing to show error,<br />loading and ready conditions.</p>
<p>Instead, (or in addition, depending on config), it should use the SVG icons like<br />the other actors do - changing them out dynamically to reflect the same states</p>
<p>This is not critical for 1.0, since the code has already been changed to draw<br />the icon to match the new icon-set design; however, it will become an issue<br />if/when the icon designs change.</p> Kepler - Bug #2338 (In Progress): TRACKING - MENUS: pop-up context menu revisionhttps://projects.ecoinformatics.org/ecoinfo/issues/23382006-01-18T22:46:32ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Tracking bug for pop-up context menu revisions - see dependency tree.<br />Replaces part of Bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: MENUS: pop-up context menu revision (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2016">#2016</a><br />See menu redesigns at:<br /><a class="external" href="http://kepler-project.org/Wiki.jsp?page=MenuAndToolBarReDesign">http://kepler-project.org/Wiki.jsp?page=MenuAndToolBarReDesign</a></p> Kepler - Bug #2337 (In Progress): TRACKING - MENUS: Top-Level Menu Revisionhttps://projects.ecoinformatics.org/ecoinfo/issues/23372006-01-18T22:15:50ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Have now got most of menus loading from a properties file. However, several<br />things yet to do, and several bugs to fix - see dependency tree.<br />Replaces part of Bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: MENUS: pop-up context menu revision (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2016">#2016</a><br />See menu redesigns at:<br /><a class="external" href="http://kepler-project.org/Wiki.jsp?page=MenuAndToolBarReDesign">http://kepler-project.org/Wiki.jsp?page=MenuAndToolBarReDesign</a></p> Kepler - Bug #2259 (In Progress): DIALOGS: Implement New Actor Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22592005-11-10T22:21:56ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New Actor Dialog, per Laura's design. See:<br /><a class="external" href="http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs">http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs</a></p> Kepler - Bug #2258 (In Progress): DIALOGS: Implement New Director Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22582005-11-10T22:20:47ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New Director Dialog, per Laura's design. See:<br /><a class="external" href="http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs">http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs</a></p> Kepler - Bug #2257 (In Progress): DIALOGS: Implement New Workflow Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22572005-11-10T22:19:40ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New Workflow Dialog, per Laura's design. See:<br /><a class="external" href="http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs">http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActorDialogs</a></p> Kepler - Bug #2245 (In Progress): TRACKING: Batik SVG Rendering - remaining taskshttps://projects.ecoinformatics.org/ecoinfo/issues/22452005-11-05T06:56:55ZMatthew Brookebrooke@nceas.ucsb.edu
<p>tasks remaining before Batik SVG rendering is ready for primetime:</p>
<p>1) ASSIGNING ICONS<br />Icons can be assigned in actor moml, or can be assigned in the actor's java<br />code. Assigning in moml means icons will show up for newly-created workflows,<br />but <strong>not</strong> for old workflows. [Note that some actors can't be set via moml (eg<br />EML200 datasource), so would need to add some to java code anyway]</p>
<p>Adding icon paths directly to the actors' java code (note that existing svg<br />icons are currently defined in java code) means icons show up for all actors, in<br />new <strong>and</strong> old workflows. Could move actual actor->svg icon mappings into a<br />separate settings file? Or would this cause too much indirection and add<br />complication?</p>
<p>2) MEMORY USAGE<br />Currently, if Batik has to display more than about 150 SVG icons, it causes a<br />JVM crash with an OutOfMemoryError. This is also an issue when showing actor<br />thumbnail icons in the actor library, since these are also rendered using Batik.<br />So for example doing a search for a very common term that returns many actors<br />(eg "a") causes an OutOfMemoryError.</p>
<p>Have looked for obvious places to save memory, but now i think we're just<br />limited by what batik can do. Obvious solution is to start caching icons, since<br />many of them may be the same, yet they all get rendered from scratch</p>
<p>3) BACKWARD-COMPATIBILITY<br /> - Need to add code so old SVG icons are translated to have their origin at the<br />top-left corner. They are currently cropped when displayed in batik, because<br />Ptolemy's default origin for svg components is at the center of each actor icon,<br />whereas the svg/batik standard is to have the origin at top-left.</p>
<p>4) TEXT WRAP:<br />In EML simple example plot, text at bottom is rendered using SVG, and it<br />does not wrap, but extends off the screen. (text did wrap in the old-style svg<br />handling). Note, however, that if annotation actor is re-created and text is<br />pasted in again, it <strong>does</strong> wrap in the new instance, so this is really just a<br />backwards-compatibility issue</p>
<p>5) SMALL ICON:<br />getIcon() method in XMLIcon works, but its success seems to be linked to the odd<br />tree refreshing behavior described in bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: unexpected workflow components tree behavior (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1843">#1843</a>. When 1843 gets fixed, we may be<br />able to make getIcon() more efficient/intuitive, and this may in turn save some<br />memory usage (see item (2) above)</p> Morpho - Bug #548 (In Progress): consolidate metadata editing systems in morphohttps://projects.ecoinformatics.org/ecoinfo/issues/5482002-07-09T15:18:24ZMatt Jonesjones@nceas.ucsb.edu
<p>The data package wizard contains a series of screens that represent modules in<br />EML. These screens can be used to edit an initial set of metadata, but then we<br />switch to the editor package to make other modifications. We need to be able to<br />use one editing environment in Morpho both in wizards and for other eidting<br />tasks. This environment needs to have the capability for a flexible layout<br />system so that it can be used in multiple contexts. We will be using work from<br />the Jalama project to accomplish this.</p>